No, it will not. If you turn it off while its saving, the AR will break, but nothing else. However the AR is fixable with the code manager software dowloadable from the codejunkies website. However there are a few gamebreaking codes, like once I typed in a code for a level 50 shiny charizard with pokerus and it wouldn't let me access my box. So I sold the game and bought black 2. You have to be careful with things like that.
Source: My Own Experience